def full(images: Images,
cors: List[ScalarCoR],
recon_params: ReconstructionParameters,
progress: Optional[Progress] = None) -> Images:
progress = Progress.ensure_instance(progress, num_steps=images.height)
output_shape = (images.num_sinograms, images.width, images.width)
output_images: Images = Images.create_empty_images(
output_shape, images.dtype, images.metadata)
output_images.record_operation('AstraRecon.full', 'Reconstruction',
**recon_params.to_dict())
# FIXME multiple GPU support - just starting up a Pool doesn't seem to work
# the GPUs can't initialise the memory properly. Not sure why
# num_gpus = AstraRecon._count_gpus()
# LOG.info(f"Running with {num_gpus} GPUs")
# partial = ptsm.create_partial(AstraRecon.single, ptsm.fwd_gpu_recon,
# num_gpus=num_gpus, cors=cors,
# proj_angles=proj_angles, recon_params=recon_params)
# ptsm.execute(images.sinograms, output_images.data, partial, num_gpus, progress=progress)
proj_angles = images.projection_angles()
for i in range(images.height):
output_images.data[i] = AstraRecon.single_sino(
images.sino(i), cors[i], proj_angles, recon_params)
progress.update(1, "Reconstructed slice")
return output_images
def full(images: Images,
cors: List[ScalarCoR],
recon_params: ReconstructionParameters,
progress: Optional[Progress] = None) -> Images:
progress = Progress.ensure_instance(progress, num_steps=images.height)
output_shape = (images.num_sinograms, images.width, images.width)
output_images: Images = Images.create_empty_images(
output_shape, images.dtype, images.metadata)
output_images.record_operation('AstraRecon.full', 'Reconstruction',
**recon_params.to_dict())
proj_angles = images.projection_angles(
recon_params.max_projection_angle)
for i in range(images.height):
output_images.data[i] = AstraRecon.single_sino(
images.sino(i), cors[i], proj_angles, recon_params)
progress.update(1, "Reconstructed slice")
return output_images
def run_preview_recon(
self, slice_idx, cor: ScalarCoR,
recon_params: ReconstructionParameters) -> Optional[Images]:
# Ensure we have some sample data
if self.images is None:
return None
# Perform single slice reconstruction
reconstructor = get_reconstructor_for(recon_params.algorithm)
output_shape = (1, self.images.width, self.images.width)
recon: Images = Images.create_empty_images(output_shape,
self.images.dtype,
self.images.metadata)
recon.data[0] = reconstructor.single_sino(
self.images.sino(slice_idx), cor,
self.images.projection_angles(recon_params.max_projection_angle),
recon_params)
recon = self._apply_pixel_size(recon, recon_params)
return recon
def test_create_empty_images(self):
images = Images.create_empty_images((15, 10, 10), np.float32, {})
self.assertEqual(images.data.shape, (15, 10, 10))